5A1I

The structure of Human MAT2A in complex with SAM, Adenosine, Methionine and PPNP.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P02PDB ENTRY 2P02

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES PH 7.5, 30 % PEG 600
Crystal Properties
Matthews coefficientSolvent content
239.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.972α = 90
b = 94.074β = 90
c = 117.216γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2014-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.173.3799.10.0924.512.3176512
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.14990.093.49.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2P021.0973.37144726751099.060.104810.103840.12398RANDOM13.035
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.460.12-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.162
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg18.214
r_sphericity_bonded12.244
r_dihedral_angle_3_deg11.93
r_dihedral_angle_1_deg6.632
r_long_range_B_refined4.369
r_long_range_B_other2.553
r_rigid_bond_restr2.308
r_scangle_other2.096
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.162
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg18.214
r_sphericity_bonded12.244
r_dihedral_angle_3_deg11.93
r_dihedral_angle_1_deg6.632
r_long_range_B_refined4.369
r_long_range_B_other2.553
r_rigid_bond_restr2.308
r_scangle_other2.096
r_angle_refined_deg1.797
r_scbond_other1.775
r_scbond_it1.773
r_mcangle_it1.145
r_mcangle_other1.145
r_angle_other_deg1.035
r_mcbond_it0.863
r_mcbond_other0.863
r_chiral_restr0.12
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2963
Nucleic Acid Atoms
Solvent Atoms515
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing